IMOD - making movies

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NOTE: This page is a daughter page of: IMOD

A couple people have asked me now how to make movies in IMOD, so I've written below a concise set of instructions. Be warned that IMOD does not actually produce any movie files. IMOD only writes a series of snapshots (one image per frame), and thus you will need a moving-making program like QuickTime Pro or Adobe Photoshop to turn this "image stack" into a movie file. Below I've shown the steps to use:

Making an Movie of the ZAP window in IMOD

  1. Open your reconstruction in 3dmod, and select the ZAP window
  2. Set the ZAP window to the desired size and zoom factor (use [+] and [-])
  3. Turn off the yellow crosshair using [shift]+[t] and toggle the model with [t]
  4. Hit [shift]+[a] to auto contrast or set the black and white to appropriate levels, and [shift]+[r] if you want the window to resize to the image
  5. Click File > Movie/Montage... to bring up the movie dialog:
  6. Set start, end, and increment to the range (and spacing) of slices you wish to capture.
  7. Set "snapshot" to "TIFF". NOTE: If "None" is selected images won't be written out.
  8. Make sure 3dmod is set to "movie mode"
  9. Middle and/or right click once anywhere inside your ZAP and it will start making your movie, and writing out a series of images "zap001.tif, zap002.tif, ..."; as shown in the main 3dmod window. Typically this is written out to whatever directory 3dmod was opened from.
  10. Once the movie is finished, open QuickTime Pro, then click File > Open Image Sequence and open the first image in the sequence; I recommend using 25 frames per second and saving as a .mov using H.264 compression (see: QuickTime - Making a Movie from an Image Sequence).

NOTE: Use the "Zap montage" option to make an image or movie larger than the size of your screen
NOTE: If you don't have Quicktime Pro see this next page to convert an image sequence to a movie (lists a few other options)

Making an Movie of the ModelView window in IMOD

  1. Open your model in 3dmod and press [v] to display the "Model View" window
  2. Select the ModelView window for all the following commands:
  3. Press [g] FOUR times to maximise Gouraud shading (makes spheres look smooth).
  4. Under "Edit" use the object list use the "Objects ..." panel to change the display (mesh/contours/points) and transparency of objects. NOTE: There are many settings here to play with
  5. Make the ModelView window the desired size, using the "Controls ..." panel to change the camera settings.
  6. With the ModelView window selected, click File > Movie (m)
  7. Use the mouse keys to set the desired starting position then click "Set Start"
  8. Use the mouse keys to change desired ending position then click "Set End"
  9. Check "write files" and then click "Make". As long as "write files" is clicked, the frames will be saved out as TIFFs - eg: (modv0000.tif, modv0001.tif, ...)
  10. Once finished, open QuickTime Pro, then click File > Open Image Sequence (see: QuickTime and/or convert an image sequence to a movie).

Unfortunately IMOD currently only supports "point-to-point" linear animation, and thus to make longer movies you must get use to clicking "Set Start" when you get to the end, then progressing to the next "step" in the movie you can use the "Objects ..." panel to manually show and hide objects as the movie progresses, but this can get a bit frustrating for making longer movies!

To make more sophisticated movies, you might like to try opening your electron tomography data in a specialized program like Amira or open your model in a professional 3D animation program such as Cinema 4D. Chimera is one of the few programs which will open and IMOD model file (.mod) directly. For most other programs you will probably have to export your model to a VRML version 1 or 2 file using the command line program imod2obj or imod2vrml... ie:

imod2vrml2 foo.mod foo.wrl

See Also